The human Y chromosome, transmitted clonally through males, contains far
fewer genes than the ***ually recombining autosome from which it evolved.
The enormity of this evolutionary decline has led to predictions that the Y
chromosome will be completely bereft of functional genes within ten million
years. Although recent evidence of gene conversion within massive Y-linked
palindromes runs counter to this hypothesis, most unique Y-linked genes are
not situated in palindromes and have no gene conversion partners. The
'impending demise' hypothesis thus rests on understanding the degree of
conservation of these genes. Here we find, by systematically comparing the
DNA sequences of unique, Y-linked genes in chimpanzee and human, which
diverged about six million years ago, evidence that in the human lineage,
all such genes were conserved through purifying selection. In the chimpanzee
lineage, by contrast, several genes have sustained inactivating mutations.
Gene decay in the chimpanzee lineage might be a consequence of positive
selection focused elsewhere on the Y chromosome and driven by sperm
competition.

Abstract and Full Text Links at Nature
http://www.nature.com/nature/journal/v437/n7055/abs/nature04101.html